Calcium in PDB 1yi7: Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum

All present enzymatic activity of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum:
3.2.1.37;

The structure of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum, PDB code: 1yi7 was solved by A.Teplyakov, E.Fedorov, G.L.Gilliland, S.C.Almo, S.K.Burley, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.130, 143.730, 188.690, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 20.2

The binding sites of Calcium atom in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum (pdb code 1yi7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum, PDB code: 1yi7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:43.2 occ:1.00 O A:GLY362 2.3 23.7 1.0 O A:ASP528 2.3 22.4 1.0 O A:ASN333 2.4 32.6 1.0 O A:HOH3171 2.5 24.1 1.0 O A:HOH3235 2.6 27.1 1.0 OD1 A:ASP528 2.6 20.4 1.0 CG A:ASP528 3.3 31.4 1.0 C A:GLY362 3.4 28.0 1.0 C A:ASP528 3.4 28.7 1.0 C A:ASN333 3.4 22.1 1.0 CA A:ASN333 3.8 26.0 1.0 OD2 A:ASP528 3.8 31.9 1.0 CA A:ASP528 3.8 30.4 1.0 CA A:GLY362 3.9 24.8 1.0 CB A:ASN333 3.9 28.3 1.0 CB A:ASP528 4.2 24.3 1.0 OD1 A:ASP335 4.5 30.2 1.0 O A:HOH3557 4.5 43.2 1.0 ND2 A:ASN333 4.5 21.3 1.0 N A:ASN363 4.5 22.2 1.0 N A:TYR529 4.5 16.5 1.0 N A:PHE334 4.6 22.4 1.0 CB A:PHE334 4.6 18.6 1.0 CG A:ASN333 4.7 23.4 1.0 CA A:TYR529 4.8 18.5 1.0 CB A:TYR529 4.9 25.1 1.0 ND2 A:ASN363 4.9 39.7 1.0 CA A:ASN363 4.9 26.9 1.0 O A:HOH3549 4.9 42.8 1.0 C A:PHE334 4.9 32.2 1.0 CA A:PHE334 5.0 30.4 1.0

Calcium binding site 2 out of 4 in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3002 b:42.9 occ:1.00 O B:GLY362 2.3 22.6 1.0 O B:ASP528 2.3 26.3 1.0 O B:HOH3162 2.4 24.1 1.0 OD1 B:ASP528 2.5 21.2 1.0 O B:ASN333 2.5 24.5 1.0 O B:HOH3358 2.6 35.5 1.0 CG B:ASP528 3.3 36.5 1.0 C B:GLY362 3.4 25.1 1.0 C B:ASP528 3.4 26.4 1.0 C B:ASN333 3.4 31.0 1.0 CA B:ASP528 3.9 26.6 1.0 CA B:ASN333 3.9 22.5 1.0 CA B:GLY362 3.9 18.8 1.0 O B:HOH3645 3.9 58.6 1.0 OD2 B:ASP528 3.9 23.9 1.0 O B:HOH3476 3.9 41.9 1.0 CB B:ASN333 4.0 22.1 1.0 CB B:ASP528 4.2 24.7 1.0 OD1 B:ASP335 4.5 41.1 1.0 N B:ASN363 4.5 23.6 1.0 N B:TYR529 4.5 20.4 1.0 N B:PHE334 4.6 14.7 1.0 ND2 B:ASN363 4.6 80.8 1.0 ND2 B:ASN333 4.6 19.8 1.0 CB B:PHE334 4.7 18.5 1.0 CA B:ASN363 4.8 28.4 1.0 CA B:TYR529 4.9 13.7 1.0 CG B:ASN333 4.9 38.9 1.0 CA B:PHE334 5.0 17.6 1.0 CB B:TYR529 5.0 24.6 1.0 C B:PHE334 5.0 32.1 1.0 O B:HOH3600 5.0 50.4 1.0

Calcium binding site 3 out of 4 in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3003 b:38.2 occ:1.00 O C:GLY362 2.2 23.7 1.0 O C:ASP528 2.3 19.2 1.0 O C:ASN333 2.4 22.4 1.0 OD1 C:ASP528 2.5 22.4 1.0 O C:HOH3133 2.6 21.8 1.0 O C:HOH3201 2.7 26.7 1.0 C C:GLY362 3.2 23.1 1.0 C C:ASP528 3.4 18.5 1.0 CG C:ASP528 3.4 31.2 1.0 C C:ASN333 3.4 25.8 1.0 CA C:ASP528 3.8 20.8 1.0 CA C:GLY362 3.8 22.7 1.0 CA C:ASN333 3.9 23.2 1.0 CB C:ASN333 4.0 26.3 1.0 OD2 C:ASP528 4.0 52.5 1.0 CB C:ASP528 4.2 22.3 1.0 N C:ASN363 4.4 25.8 1.0 OD1 C:ASP335 4.4 39.8 1.0 N C:PHE334 4.5 20.3 1.0 N C:TYR529 4.5 18.7 1.0 ND2 C:ASN333 4.6 24.4 1.0 CB C:PHE334 4.6 19.4 1.0 ND2 C:ASN363 4.7 36.6 1.0 O C:HOH3406 4.7 38.0 1.0 CA C:ASN363 4.7 23.7 1.0 CG C:ASN333 4.8 24.7 1.0 C C:PHE334 4.9 28.9 1.0 CA C:TYR529 4.9 12.3 1.0 CA C:PHE334 4.9 20.6 1.0 O C:HOH3649 4.9 50.6 1.0 O C:PHE334 5.0 22.1 1.0

Calcium binding site 4 out of 4 in the Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Beta-D-Xylosidase (Selenomethionine) Xynd From Clostridium Acetobutylicum within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca3004 b:41.1 occ:1.00 O D:GLY362 2.3 25.1 1.0 O D:ASP528 2.3 20.8 1.0 O D:ASN333 2.4 21.4 1.0 O D:HOH3273 2.5 30.8 1.0 O D:HOH3218 2.5 27.0 1.0 OD1 D:ASP528 2.6 19.8 1.0 C D:ASN333 3.3 15.9 1.0 C D:GLY362 3.3 20.8 1.0 C D:ASP528 3.4 26.9 1.0 CG D:ASP528 3.4 27.9 1.0 CA D:ASN333 3.8 21.4 1.0 CA D:ASP528 3.9 26.9 1.0 CA D:GLY362 3.9 15.5 1.0 CB D:ASN333 3.9 17.0 1.0 OD2 D:ASP528 4.0 42.5 1.0 ND2 D:ASN363 4.2 35.7 1.0 CB D:ASP528 4.2 23.6 1.0 ND2 D:ASN333 4.4 18.4 1.0 O D:HOH3400 4.4 38.1 1.0 N D:PHE334 4.5 21.0 1.0 N D:ASN363 4.5 20.1 1.0 N D:TYR529 4.5 24.9 1.0 OD1 D:ASP335 4.5 80.4 1.0 CG D:ASN333 4.7 22.9 1.0 CB D:PHE334 4.7 19.6 1.0 CA D:ASN363 4.8 19.0 1.0 CA D:TYR529 4.9 14.9 1.0 CB D:TYR529 4.9 15.2 1.0 C D:PHE334 4.9 20.5 1.0 CA D:PHE334 4.9 20.4 1.0 O D:PHE334 5.0 22.6 1.0

A.Teplyakov, E.Fedorov, G.L.Gilliland, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc). Crystal Structure of Beta-Xylosidase From Clostridium Acetobutylicum To Be Published.